The generic name Arsinoitherium comes from Queen Arsinoe after whom the Fayum, the region in which the fossils were found, was called during Ptolemaic times, and the Greek: θηρίον (therion), "beast". The species epithet of the type species, A. zitteli, was given to it in honor of the eminent german paleontologist Karl Alfred von Zittel, regarded by some as the pioneer of paleontology in Egypt.